From 1579a88b32b33a12ed391384c55bb3bfe036d7a9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 21 Jul 2016 19:35:31 +0200
Subject: [PATCH] Split methods
---
.../lumc/sasc/biopet/tools/bamstats/BamStats.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/bamstats/Stats.scala | 3 ++-
.../biopet/tools/flagstat/BiopetFlagstat.scala | 2 +-
.../biopet/tools/flagstat/FlagstatCollector.scala | 14 +++++++++++++-
4 files changed, 17 insertions(+), 4 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
index 4b39411da..6509e9cdb 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
@@ -77,7 +77,7 @@ object BamStats extends ToolCommand {
}
/**
- * This is the main running function of [[BamStats]]. This will start the thereads and collect and write the results.
+ * This is the main running function of [[BamStats]]. This will start the threads and collect and write the results.
*
* @param outputDir All output files will be placed here
* @param bamFile Input bam file
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
index 394ccb8dd..6f6aa43c4 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
@@ -17,7 +17,8 @@ case class Stats(flagstat: FlagstatCollector = new FlagstatCollector(),
_3_ClippingHistogram: Histogram[Int] = new Histogram[Int]()) {
flagstat.loadDefaultFunctions()
- flagstat.loadAditionalFunctions(1, 0)
+ flagstat.loadQualityFunctions(1, 0)
+ flagstat.loadOrientationFunctions
/** This will add an other [[Stats]] inside `this` */
def +=(other: Stats): Stats = {
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
index 193d6ce80..9ba72c3ff 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
@@ -62,7 +62,7 @@ object BiopetFlagstat extends ToolCommand {
val flagstatCollector = new FlagstatCollector
flagstatCollector.loadDefaultFunctions()
- flagstatCollector.loadAditionalFunctions()
+ flagstatCollector.loadQualityFunctions()
logger.info("Start reading file: " + commandArgs.inputFile)
for (record <- iterSam) {
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
index 693bf849a..f24d04e38 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
@@ -40,9 +40,21 @@ class FlagstatCollector {
addFunction("SecondaryOrSupplementary", record => record.isSecondaryOrSupplementary)
}
- def loadAditionalFunctions(m: Int = 10, max: Int = 60): Unit = {
+ /**
+ * The method will aditional checks based on mapping quality of the sam records.
+ *
+ * @param m steps of qaulity
+ * @param max maximum quality
+ */
+ def loadQualityFunctions(m: Int = 10, max: Int = 60): Unit = {
for (t <- 0 to (max / m))
this.addFunction("MAPQ>" + (t * m), record => record.getMappingQuality > (t * m))
+ }
+
+ /**
+ * This method will add functions to check orientation, for this a combination of flags and read positions are used.
+ */
+ def loadOrientationFunctions = {
this.addFunction("First normal, second read inverted (paired end orientation)", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
--
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